Практическое задание 8

Плискин Александр
In [1]:
import sys 
import modeller 
import _modeller
import modeller.automodel
import nglview # в HTML nglview не отображается, поэтому добавляю скрины
import ipywidgets

from IPython.display import Image
In [2]:
env=modeller.environ()
env.io.hetatm=True
                         MODELLER 9.23, 2019/10/22, r11522

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                     Copyright(c) 1989-2019 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
              B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
          M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
             A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
                     F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK


Kind, OS, HostName, Kernel, Processor: 4, Darwin MacBook-Pro-Aleksandr.local 19.0.0 x86_64
Date and time of compilation         : 2019/10/22 14:53:24
MODELLER executable type             : mac10v4-intel64
Job starting time (YY/MM/DD HH:MM:SS): 2019/11/20 23:55:11

In [3]:
! wget http://files.rcsb.org/view/1lmp.pdb
! wget https://www.uniprot.org/uniprot/P61626.fasta # лизоцим человека
--2019-11-20 23:55:12--  http://files.rcsb.org/view/1lmp.pdb
Распознаётся files.rcsb.org (files.rcsb.org)… 128.6.244.12
Подключение к files.rcsb.org (files.rcsb.org)|128.6.244.12|:80... соединение установлено.
HTTP-запрос отправлен. Ожидание ответа… 200 OK
Длина: нет данных [text/plain]
Сохранение в: «1lmp.pdb»

1lmp.pdb                [     <=>            ] 127,35K   116KB/s    за 1,1s    

2019-11-20 23:55:15 (116 KB/s) - «1lmp.pdb» сохранён [130410]

--2019-11-20 23:55:15--  https://www.uniprot.org/uniprot/P61626.fasta
Распознаётся www.uniprot.org (www.uniprot.org)… 193.62.192.81, 128.175.245.185
Подключение к www.uniprot.org (www.uniprot.org)|193.62.192.81|:443... соединение установлено.
HTTP-запрос отправлен. Ожидание ответа… 200 
Длина: 225 [text/plain]
Сохранение в: «P61626.fasta»

P61626.fasta        100%[===================>]     225  --.-KB/s    за 0s      

2019-11-20 23:55:15 (23,8 MB/s) - «P61626.fasta» сохранён [225/225]

In [4]:
nglview.show_structure_file('1lmp.pdb')
In [5]:
Image(filename = '1.png', width=1000, height=1000)
Out[5]:
In [6]:
alignm = modeller.alignment(env)

alignm.append(file='P61626.fasta', align_codes='all', alignment_format='FASTA')

mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
alignm[0].code = 'P61626'

alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')

s = alignm[0]
pdb = alignm[1]

print(s.code, pdb.code)

a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns=pdb.code, sequence=s.code)
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
read_pd_459W> Residue type  NAG not recognized. 'automodel' model building
              will treat this residue as a rigid body.
              To use real parameters, add the residue type to ${LIB}/restyp.lib,
              its topology to ${LIB}/top_*.lib, and suitable forcefield
              parameters to ${LIB}/par.lib.
rdpdb___459W> Residue type  NDG not recognized. 'automodel' model building
              will treat this residue as a rigid body.
              To use real parameters, add the residue type to ${LIB}/restyp.lib,
              its topology to ${LIB}/top_*.lib, and suitable forcefield
              parameters to ${LIB}/par.lib.

SALIGN_____> adding the next group to the alignment; iteration    1
P61626 1lmp
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)

check_ali___> Checking the sequence-structure alignment. 

Implied intrachain target CA(i)-CA(i+1) distances longer than  8.0 angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file:        3
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL:        4
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    13194    12190


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      148
Number of all, selected real atoms                :     1157    1157
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    12190   12190
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2320
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         806.5338





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1177       0      0   0.006   0.006      12.181       1.000
 2 Bond angle potential               :    1592       0      8   2.105   2.105      141.57       1.000
 3 Stereochemical cosine torsion poten:     738       0     29  48.051  48.051      269.35       1.000
 4 Stereochemical improper torsion pot:     481       0      0   1.338   1.338      19.372       1.000
 5 Soft-sphere overlap restraints     :    2320       0      0   0.002   0.002     0.78071       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2405       0      0   0.129   0.129      42.583       1.000
10 Distance restraints 2 (N-O)        :    2564       0      0   0.148   0.148      64.649       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     147       0      3   4.238   4.238      31.135       1.000
14 Sidechain Chi_1 dihedral restraints:     120       0      0  62.610  62.610      14.898       1.000
15 Sidechain Chi_2 dihedral restraints:      86       0      1  73.786  73.786      37.192       1.000
16 Sidechain Chi_3 dihedral restraints:      35       0      0  81.302  81.302      27.332       1.000
17 Sidechain Chi_4 dihedral restraints:      20       0      0 106.388 106.388      15.681       1.000
18 Disulfide distance restraints      :       4       0      0   0.007   0.007     0.35628E-01   1.000
19 Disulfide angle restraints         :       8       0      0   1.584   1.584     0.44306       1.000
20 Disulfide dihedral angle restraints:       4       0      0  27.448  27.448      2.8808       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1691       0      0   0.410   0.410      35.097       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     146      15     19  21.904  58.099      26.728       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     972       0      1   0.660   0.660      64.628       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: P61626.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   14696.8633



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4005   1M   2K C   N       7    9  -68.47  -70.20   14.68    1.10  -62.90  164.32   21.65
    1          2K   2K N   CA      9   10  154.97  140.40                  -40.80
    2   4006   2K   3A C   N      16   18  -65.05  -68.20   15.17    1.33  -62.50  158.98   26.18
    2          3A   3A N   CA     18   19  160.14  145.30                  -40.90
    3   4007   3A   4L C   N      21   23  -71.30  -70.70   14.60    1.08  -63.50  162.80   23.06
    3          4L   4L N   CA     23   24  156.19  141.60                  -41.20
    4   4010   6V   7L C   N      44   46 -131.72 -108.50   28.56    1.26  -63.50 -177.14   29.61
    4          7L   7L N   CA     46   47  149.14  132.50                  -41.20
    5   4011   7L   8G C   N      52   54 -109.49  -80.20   75.14    4.39   82.20 -166.04   15.13
    5          8G   8G N   CA     54   55  104.90  174.10                    8.50
    6   4012   8G   9L C   N      56   58 -168.79 -108.50   60.53    2.82  -63.50 -152.16   25.48
    6          9L   9L N   CA     58   59  138.00  132.50                  -41.20
    7   4014  10V  11L C   N      71   73 -126.81 -108.50   19.59    0.87  -63.50 -169.84   30.32
    7         11L  11L N   CA     73   74  139.49  132.50                  -41.20
    8   4015  11L  12L C   N      79   81 -111.13 -108.50   62.31    3.39  -63.50  121.20   14.92
    8         12L  12L N   CA     81   82   70.25  132.50                  -41.20
    9   4016  12L  13S C   N      87   89  176.95 -136.60   48.16    2.24  -64.10 -149.66   14.61
    9         13S  13S N   CA     89   90  138.47  151.20                  -35.00
   10   4018  14V  15T C   N     100  102 -142.33 -124.80   41.53    1.34  -63.20  158.00   25.33
   10         15T  15T N   CA    102  103 -178.85  143.50                  -42.10
   11   4020  16V  17Q C   N     114  116  -74.16  -73.00    8.86    0.56  -63.80  170.53   25.62
   11         17Q  17Q N   CA    116  117  149.48  140.70                  -40.30
   12   4021  17Q  18G C   N     123  125 -142.87 -167.20   42.69    1.16   82.20 -171.93   14.46
   12         18G  18G N   CA    125  126  139.51  174.60                    8.50
   13   4022  18G  19K C   N     127  129  -80.57  -70.20   10.74    0.72  -62.90  176.90   23.98
   13         19K  19K N   CA    129  130  143.18  140.40                  -40.80
   14   4057  53E  54S C   N     415  417 -138.88  -64.10   82.48    8.72  -64.10   82.48    8.72
   14         54S  54S N   CA    417  418   -0.19  -35.00                  -35.00
   15   4069  65A  66G C   N     508  510  -66.35  -62.40    5.15    0.96   82.20  157.73   12.02
   15         66G  66G N   CA    510  511  -44.50  -41.20                    8.50


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0    0    6   33   69  108  112  121  161  195  167


<< end of ENERGY.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      148
Number of all, selected real atoms                :     1157    1157
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    12190   12190
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2316
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         760.9730





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1177       0      0   0.006   0.006      10.702       1.000
 2 Bond angle potential               :    1592       0      5   2.009   2.009      131.51       1.000
 3 Stereochemical cosine torsion poten:     738       0     29  48.507  48.507      275.08       1.000
 4 Stereochemical improper torsion pot:     481       0      0   1.360   1.360      19.850       1.000
 5 Soft-sphere overlap restraints     :    2316       0      0   0.001   0.001     0.32937       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2405       0      0   0.115   0.115      29.571       1.000
10 Distance restraints 2 (N-O)        :    2564       0      0   0.147   0.147      62.661       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     147       0      2   4.265   4.265      31.537       1.000
14 Sidechain Chi_1 dihedral restraints:     120       0      2  65.124  65.124      24.195       1.000
15 Sidechain Chi_2 dihedral restraints:      86       0      0  57.168  57.168      28.174       1.000
16 Sidechain Chi_3 dihedral restraints:      35       0      0  80.372  80.372      22.809       1.000
17 Sidechain Chi_4 dihedral restraints:      20       0      0 111.815 111.815      13.449       1.000
18 Disulfide distance restraints      :       4       0      0   0.008   0.008     0.49387E-01   1.000
19 Disulfide angle restraints         :       8       0      0   2.309   2.309     0.94215       1.000
20 Disulfide dihedral angle restraints:       4       0      0  23.384  23.384      2.2667       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1691       0      0   0.405   0.405      34.056       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     146      15     15  21.018  56.634      25.441       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     972       0      0   0.596   0.596      48.354       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: P61626.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   13973.9248



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4005   1M   2K C   N       7    9  -64.28  -70.20   11.00    0.67  -62.90  171.94   22.25
    1          2K   2K N   CA      9   10  131.13  140.40                  -40.80
    2   4006   2K   3A C   N      16   18 -129.39 -134.00    5.29    0.12  -62.50 -172.94   34.23
    2          3A   3A N   CA     18   19  144.41  147.00                  -40.90
    3   4007   3A   4L C   N      21   23 -108.03 -108.50    3.55    0.20  -63.50 -177.27   23.22
    3          4L   4L N   CA     23   24  136.02  132.50                  -41.20
    4   4010   6V   7L C   N      44   46  -75.88  -70.70   28.70    2.38  -63.50  155.07   20.85
    4          7L   7L N   CA     46   47  113.37  141.60                  -41.20
    5   4011   7L   8G C   N      52   54   77.79   78.70   20.98    0.64   82.20  164.49    7.76
    5          8G   8G N   CA     54   55  172.94 -166.10                    8.50
    6   4012   8G   9L C   N      56   58 -109.90 -108.50   22.99    1.26  -63.50  157.74   19.78
    6          9L   9L N   CA     58   59  109.56  132.50                  -41.20
    7   4014  10V  11L C   N      71   73 -130.38 -108.50   24.29    1.07  -63.50 -171.96   30.25
    7         11L  11L N   CA     73   74  143.05  132.50                  -41.20
    8   4015  11L  12L C   N      79   81  -88.34 -108.50   68.37    3.45  -63.50  111.18   14.21
    8         12L  12L N   CA     81   82   67.17  132.50                  -41.20
    9   4016  12L  13S C   N      87   89  165.76 -136.60   62.92    1.97  -64.10 -162.50   23.67
    9         13S  13S N   CA     89   90  176.43  151.20                  -35.00
   10   4018  14V  15T C   N     100  102 -128.92 -124.80    5.67    0.19  -63.20 -177.27   27.77
   10         15T  15T N   CA    102  103  147.40  143.50                  -42.10
   11   4020  16V  17Q C   N     114  116 -117.55 -121.10   11.16    0.57  -63.80  177.74   29.00
   11         17Q  17Q N   CA    116  117  150.28  139.70                  -40.30
   12   4021  17Q  18G C   N     123  125   60.96   78.70   28.93    0.52   82.20  153.23    8.49
   12         18G  18G N   CA    125  126 -143.25 -166.10                    8.50
   13   4022  18G  19K C   N     127  129 -130.82 -118.00   13.69    0.61  -62.90 -172.18   21.74
   13         19K  19K N   CA    129  130  134.31  139.10                  -40.80
   14   4057  53E  54S C   N     415  417 -136.69  -64.10   81.41    8.42  -64.10   81.41    8.42
   14         54S  54S N   CA    417  418    1.87  -35.00                  -35.00
   15   4069  65A  66G C   N     508  510  -66.83  -62.40    5.34    1.01   82.20  158.08   12.04
   15         66G  66G N   CA    510  511  -44.19  -41.20                    8.50


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0    5    7   43   73   92  106  122  135  177  201


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
P61626.B99990001.pdb           806.53381
P61626.B99990002.pdb           760.97296

In [7]:
! cat all_in_one.ali
>P1;P61626
sequence::     : :     : :::-1.00:-1.00
MKALIVLGLVLLSVTVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIF
QINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV--
-*

>P1;1lmp
structureX:1lmp.pdb:   1 :A:+132 :A:MOL_ID  1; MOLECULE  LYSOZYME; CHAIN  A; SYNONYM  MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC  3.2.1.17:MOL_ID  1; ORGANISM_SCIENTIFIC  ONCORHYNCHUS MYKISS; ORGANISM_COMMON  RAINBOW TROUT; ORGANISM_TAXID  8022; ORGAN  KIDNEY: 2.00: 0.16
------------------KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNT-DGSTDYGIF
QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV..
.*
In [8]:
nglview.show_structure_file('P61626.B99990001.pdb') # лиганда нет
In [9]:
Image(filename = '2.png', width=1000, height=1000)
Out[9]:
In [10]:
nglview.show_structure_file('P61626.B99990002.pdb')
In [11]:
Image(filename = '3.png', width=1000, height=1000)
Out[11]:
In [12]:
alignm[1].residues[129:]
Out[12]:
[Residue 130:A (type NAG), Residue 131:A (type NAG), Residue 132:A (type NDG)]

Добавим к лизоциму человека лиганд, дописав три точки в конце

In [13]:
lig = ''
for i in alignm[0].residues:
    lig += i.code
lig += '...'
In [14]:
lig
Out[14]:
'MKALIVLGLVLLSVTVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV...'
In [15]:
alignm.append_sequence(lig)
alignm[2].code = 'ligand'
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration    1

SALIGN_____> adding the next group to the alignment; iteration    2
In [16]:
## Выбираем объект для моделирования 
s = alignm[2]
pdb = alignm[1]

print(s.code, pdb.code)

## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= pdb.code , sequence = s.code )
a.name='mod'+s.code
a.starting_model = 1
a.ending_model = 2
a.make()
ligand 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
                be used instead of the automodel defaults. If this is not what you
                want, clear them before creating the automodel object with
                env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)

check_ali___> Checking the sequence-structure alignment. 

Implied intrachain target CA(i)-CA(i+1) distances longer than  8.0 angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
END OF TABLE

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:    18   148
              atom names           : C     +N
              atom indices         :  1155     0

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:    18   148
              atom names           : C     CA    +N    O
              atom indices         :  1155  1151     0  1156
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL:        4
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    14595    13591


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      151
Number of all, selected real atoms                :     1200    1200
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    13591   13591
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2555
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :         923.5734





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1177       0      0   0.006   0.006      12.949       1.000
 2 Bond angle potential               :    1592       0      8   2.179   2.179      154.04       1.000
 3 Stereochemical cosine torsion poten:     738       0     26  47.429  47.429      262.23       1.000
 4 Stereochemical improper torsion pot:     481       0      1   1.507   1.507      23.567       1.000
 5 Soft-sphere overlap restraints     :    2555       2      2   0.008   0.008      17.449       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2405       0      0   0.126   0.126      35.579       1.000
10 Distance restraints 2 (N-O)        :    2564       0      3   0.179   0.179      86.466       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     147       0      4   4.869   4.869      41.090       1.000
14 Sidechain Chi_1 dihedral restraints:     120       0      3  66.903  66.903      29.155       1.000
15 Sidechain Chi_2 dihedral restraints:      86       0      0  73.224  73.224      36.187       1.000
16 Sidechain Chi_3 dihedral restraints:      35       0      0  86.942  86.942      24.469       1.000
17 Sidechain Chi_4 dihedral restraints:      20       0      0  78.970  78.970      13.808       1.000
18 Disulfide distance restraints      :       4       0      0   0.013   0.013     0.10938       1.000
19 Disulfide angle restraints         :       8       0      0   2.753   2.753      1.3384       1.000
20 Disulfide dihedral angle restraints:       4       0      0  20.817  20.817      1.7306       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1691       0      0   0.441   0.441      46.213       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     146      18     21  20.397  62.746      40.277       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     972       0      0   0.742   0.742      82.887       1.000
27 Distance restraints 5 (X-Y)        :    1401       0      0   0.033   0.033      14.025       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: ligand.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   15572.4893



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4005   1M   2K C   N       7    9  -78.66  -70.20   21.93    1.39  -62.90  159.35   21.59
    1          2K   2K N   CA      9   10  160.63  140.40                  -40.80
    2   4006   2K   3A C   N      16   18  -68.51  -68.20   13.00    1.04  -62.50  160.91   26.67
    2          3A   3A N   CA     18   19  158.30  145.30                  -40.90
    3   4007   3A   4L C   N      21   23  -66.13  -70.70    9.17    0.86  -63.50  169.27   23.65
    3          4L   4L N   CA     23   24  149.55  141.60                  -41.20
    4   4010   6V   7L C   N      44   46  -54.02  -70.70   20.46    1.40  -63.50  171.22   24.33
    4          7L   7L N   CA     46   47  129.75  141.60                  -41.20
    5   4011   7L   8G C   N      52   54  169.34 -167.20   28.65    0.98   82.20  173.16   12.28
    5          8G   8G N   CA     54   55  158.15  174.60                    8.50
    6   4012   8G   9L C   N      56   58 -108.17 -108.50    9.27    0.50  -63.50 -177.42   28.09
    6          9L   9L N   CA     58   59  141.76  132.50                  -41.20
    7   4014  10V  11L C   N      71   73 -121.89 -108.50   21.89    1.01  -63.50  178.79   28.43
    7         11L  11L N   CA     73   74  149.81  132.50                  -41.20
    8   4015  11L  12L C   N      79   81 -103.65 -108.50    4.88    0.23  -63.50  177.77   22.71
    8         12L  12L N   CA     81   82  131.97  132.50                  -41.20
    9   4016  12L  13S C   N      87   89 -160.32 -136.60   35.20    1.16  -64.10  176.34   19.72
    9         13S  13S N   CA     89   90  177.21  151.20                  -35.00
   10   4017  13S  14V C   N      93   95  -60.73  -62.40    7.76    0.90 -125.40  178.83   10.07
   10         14V  14V N   CA     95   96  -49.97  -42.40                  143.30
   11   4018  14V  15T C   N     100  102 -102.45  -78.10   55.44    1.82  -63.20  124.64   18.59
   11         15T  15T N   CA    102  103 -160.40  149.80                  -42.10
   12   4020  16V  17Q C   N     114  116 -137.28 -121.10   23.95    1.23  -63.80  178.20   23.16
   12         17Q  17Q N   CA    116  117  122.04  139.70                  -40.30
   13   4021  17Q  18G C   N     123  125  -99.14  -80.20   35.32    0.85   82.20 -117.08    7.96
   13         18G  18G N   CA    125  126 -156.09  174.10                    8.50
   14   4022  18G  19K C   N     127  129  -64.66  -70.20   21.96    1.46  -62.90  159.96   20.68
   14         19K  19K N   CA    129  130  119.15  140.40                  -40.80
   15   4057  53E  54S C   N     415  417 -133.61  -64.10   74.84    8.18  -64.10   74.84    8.18
   15         54S  54S N   CA    417  418   -7.25  -35.00                  -35.00
   16   4069  65A  66G C   N     508  510  -73.89  -62.40   11.70    2.17   82.20  164.51   12.48
   16         66G  66G N   CA    510  511  -43.43  -41.20                    8.50
   17   4138 134C 135Q C   N    1043 1045  -56.74  -63.80   15.53    2.00  -73.00  165.97   11.18
   17        135Q 135Q N   CA   1045 1046  -54.13  -40.30                  140.70
   18   4139 135Q 136N C   N    1052 1054 -113.88 -119.90   68.91    2.99   55.90  172.21   17.81
   18        136N 136N N   CA   1054 1055   68.35  137.00                   39.50


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0   11    9   44   88  136  100  148  165  193  217


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      151
Number of all, selected real atoms                :     1200    1200
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    13591   13591
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2556
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1085.2201





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1177       0      0   0.007   0.007      14.333       1.000
 2 Bond angle potential               :    1592       0      9   2.314   2.314      171.55       1.000
 3 Stereochemical cosine torsion poten:     738       0     21  47.450  47.450      264.45       1.000
 4 Stereochemical improper torsion pot:     481       0      1   1.586   1.586      25.491       1.000
 5 Soft-sphere overlap restraints     :    2556       1      2   0.008   0.008      17.718       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2405       0      0   0.146   0.146      54.839       1.000
10 Distance restraints 2 (N-O)        :    2564       2     14   0.218   0.218      140.92       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     147       0      3   4.854   4.854      40.845       1.000
14 Sidechain Chi_1 dihedral restraints:     120       0      4  73.034  73.034      45.359       1.000
15 Sidechain Chi_2 dihedral restraints:      86       0      0  70.518  70.518      41.328       1.000
16 Sidechain Chi_3 dihedral restraints:      35       0      0 102.766 102.766      27.051       1.000
17 Sidechain Chi_4 dihedral restraints:      20       0      0  84.330  84.330      12.436       1.000
18 Disulfide distance restraints      :       4       0      0   0.013   0.013     0.11141       1.000
19 Disulfide angle restraints         :       8       0      0   1.891   1.891     0.63174       1.000
20 Disulfide dihedral angle restraints:       4       0      0  31.260  31.260      3.7639       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1691       0      0   0.488   0.488      62.885       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     146      17     19  20.524  63.919      37.847       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     972       0      4   0.855   0.855      108.74       1.000
27 Distance restraints 5 (X-Y)        :    1401       0      0   0.034   0.034      14.922       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: ligand.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   16882.2070



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature 10                           : Distance restraints 2 (N-O)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   7443  45N  38Y N   O     336  293   11.74    9.41    2.33    4.90    9.41    2.33    4.90
    2   7472  46W  38Y N   O     344  293   11.04    8.62    2.42    5.47    8.62    2.42    5.47

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4005   1M   2K C   N       7    9  -68.61  -70.20    7.55    0.58  -62.90  171.52   22.59
    1          2K   2K N   CA      9   10  147.78  140.40                  -40.80
    2   4006   2K   3A C   N      16   18  -64.15  -68.20    5.45    0.54  -62.50  170.16   27.97
    2          3A   3A N   CA     18   19  148.95  145.30                  -40.90
    3   4007   3A   4L C   N      21   23  -67.94  -70.70    7.72    0.50  -63.50  175.65   24.14
    3          4L   4L N   CA     23   24  134.39  141.60                  -41.20
    4   4010   6V   7L C   N      44   46  -95.84 -108.50   14.44    0.78  -63.50 -177.75   27.26
    4          7L   7L N   CA     46   47  139.44  132.50                  -41.20
    5   4011   7L   8G C   N      52   54   88.77   78.70   28.12    0.44   82.20  159.28    8.06
    5          8G   8G N   CA     54   55  167.65 -166.10                    8.50
    6   4012   8G   9L C   N      56   58 -106.24 -108.50    6.01    0.30  -63.50  173.48   22.03
    6          9L   9L N   CA     58   59  126.93  132.50                  -41.20
    7   4014  10V  11L C   N      71   73  -98.02 -108.50   27.85    1.37  -63.50  151.88   19.39
    7         11L  11L N   CA     73   74  106.70  132.50                  -41.20
    8   4015  11L  12L C   N      79   81 -105.18 -108.50   22.39    1.17  -63.50  157.19   19.86
    8         12L  12L N   CA     81   82  110.36  132.50                  -41.20
    9   4016  12L  13S C   N      87   89 -160.96 -136.60   35.33    1.16  -64.10  177.05   19.82
    9         13S  13S N   CA     89   90  176.79  151.20                  -35.00
   10   4018  14V  15T C   N     100  102 -142.77 -124.80   27.74    0.87  -63.20  172.69   27.30
   10         15T  15T N   CA    102  103  164.63  143.50                  -42.10
   11   4020  16V  17Q C   N     114  116 -138.65 -121.10   17.78    0.61  -63.80 -167.69   32.22
   11         17Q  17Q N   CA    116  117  142.55  139.70                  -40.30
   12   4022  18G  19K C   N     127  129 -127.25 -118.00   19.26    0.77  -62.90  175.44   26.63
   12         19K  19K N   CA    129  130  155.99  139.10                  -40.80
   13   4041  37G  38Y C   N     280  282  -60.23  -63.50   12.51    1.83  -98.40 -179.78   18.61
   13         38Y  38Y N   CA    282  283  -55.47  -43.40                  128.40
   14   4042  38Y  39R C   N     292  294 -123.59 -125.20   86.30    4.13   57.30  179.85   21.51
   14         39R  39R N   CA    294  295   54.31  140.60                   38.00
   15   4069  65A  66G C   N     508  510  -73.03  -62.40   10.63    1.89   82.20  162.90   12.32
   15         66G  66G N   CA    510  511  -40.90  -41.20                    8.50
   16   4138 134C 135Q C   N    1043 1045  -54.82  -63.80   15.61    2.00  -73.00  167.22   11.31
   16        135Q 135Q N   CA   1045 1046  -53.07  -40.30                  140.70
   17   4139 135Q 136N C   N    1052 1054 -122.19 -119.90   66.43    3.07   55.90 -179.22   18.65
   17        136N 136N N   CA   1054 1055   70.61  137.00                   39.50


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    1    6    9   37   85  123  128  151  159  191  200


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
ligand.B99990001.pdb           923.57343
ligand.B99990002.pdb          1085.22009

In [17]:
nglview.show_structure_file('ligand.B99990001.pdb')
In [18]:
nglview.show_structure_file('ligand.B99990002.pdb')
In [19]:
Image(filename = '4.png', width=1000, height=1000)
Out[19]:

После добавления лиганда nglview отображает некрасиво, поэтому открывал в PyMOL

In [20]:
Image(filename = '5.png', width=1000, height=1000)
Out[20]:
In [21]:
Image(filename = '6.png', width=1000, height=1000)
Out[21]: